Combination vaccines against Mycobacterium sp. and methods of using the same

ABSTRACT

The invention relates to a combination vaccine against  Mycobacterium avium  subspecies  paratuberculosis  (MAP) and  M. tuberculosis  and/or  M. bovis  for use in methods of immunizing a subject against mycobacterial infection, preventing or treating mycobacterial infection, and preventing a disease associated with mycobacterial infection.

INTRODUCTION

This application is a continuation-in-part application of U.S. patent application Ser. No. 12/108,144, filed Apr. 23, 2008, now U.S. Pat. No. 7,846,420, which claims benefit of priority to U.S. Provisional Patent Application Ser. No. 60/913,315, filed Apr. 23, 2007, the contents of which are incorporated herein by reference in their entireties.

BACKGROUND OF THE INVENTION

Johne's disease is a chronic diarrheal enteric disease in ruminants that is caused by Mycobacterium avium subspecies paratuberculosis (MAP)(Johne & Frothingham (1895) Dtsch. Zeitschr. Tiermed. Vergl. Pathol. 21:438-454). Live MAP is shed into the milk of cows with Johne's disease (Sweeney (1996) Vet. Clin. North Am. Food Anim. Pract. 12(2):305-12). MAP has been cultured from commercially available pasteurized milk in Europe and the United States (Grant (1998) Appl. Environ. Microbiol. 64(7):2760-1; Ellingson, et al. (2005) J. Food Prot. 68(5):966-72). When Crohn's disease was first described (Crohn, et al. (1932) J. Amer. Med. Assoc. 99:1323-1328), similarities to Johne's disease were identified (Dalziel (1913) Br. Med. J. ii:1068-1070). However, in humans MAP exists in the cell wall-deficient form (Chiodini (1987) J. Clin. Microbiol. 25:796-801). Therefore, in the early analysis of Crohn's disease, MAP could not be detected in humans by the mycobacterial identification techniques of the time, because such techniques stained the mycobacterial cell wall (Ziehl (1882) Dtsch. Med. Wschr. 8:451; Neelsen (1883) Zbl. Med. Wiss. 21:497-501). However, since 1913 the presence of MAP has been identified in humans by other means (see, e.g., Greenstein (2003) Lancet Infect. Dis. 3(8):507-14) and an infectious etiology has been posited for some (Hermon-Taylor (1998) Ital. J. Gastroenterol. Hepatol. 30(6):607-10; Borody, et al. (2002) Dig. Liver Dis. 34(1):29-38), or all (Greenstein (2005) Genetics, Barrier Function, Immunologic & Microbial Pathways. Munster, Germany:25) of inflammatory bowel disease (IBD).

Since the first detection of MAP RNA (Mishina, et al. (1996) Proc. Natl. Acad. Sci. USA 93(18):9816-9820), MAP has been suggested as being the primary and unique, etiological agent of all IBD (Naser, et al. (2004) Lancet 364(9439):1039-1044; Autschbach, et al. (2005) Gut 54(7):944-9; Greenstein (2005) supra; Greenstein (2005) Genetics, Barrier Function, Immunologic & Microbial Pathways. Munster, Germany:24; Greenstein (2005) Crohn's and Colitis Foundation (CCFA) National Research and Clinical Conference. Fourth Annual Advances in Inflammatory Bowel Disease. Miami, Fla.:211) including Perforating and Non-perforating Crohn's disease (Greenstein, et al. (1988) GUT 29:588-592; Gilberts, et al. (1994) Proc. Natl. Acad. Sci. USA 91(126):12721-12724) and ulcerative colitis. It is believed that the particular clinical presentation of IBD that manifests is dependent upon the infected individual's immune response to MAP (Gilberts, et al. (1994) supra). This is analogous to another mycobacterial disease, leprosy. There are two clinical forms of leprosy, tuberculoid and lepromatous (Hansen (1874) Norsk Magazin Laegevidenskaben 4:1-88), both of which are caused by the same organism, M. leprae. The form of leprosy that manifests in a given individual is determined by the immune response of the infected patient (Yamamura, et al. (1991) Science 254:277-279), not by the phenotype or genotype of the leprosy bacillus.

It has been suggested that Koch's postulates (Koch (1882) Berl. Klin. Wschr. 19:221-230), originally promulgated for use in demonstrating tuberculosis infection, may have been met for MAP in Crohn's disease (Greenstein (2003) supra) and more recently for MAP in ulcerative colitis (Greenstein (2005) supra; Naser, et al. (2004) supra).

The link between MAP infection and other diseases is under investigation. An association between ulcerative colitis and Multiple Sclerosis has been suggested (Rang, et al. (1982) The Lancet pg. 555) and the positive association between IBD incidence rates and Multiple Sclerosis has led to the suggestion that these two chronic, immunologically-mediated diseases may have a common environmental etiology (Green, et al. (2006) Am. J. Epidemiol. 164(7):615-23). However, the common causal agent of ulcerative colitis and Multiple Sclerosis was not identified. Moreover, while the symptoms of Multiple Sclerosis have been ameliorated with variety of therapeutic agents including azathioprine, methotrexate, cyclophosphamide and mitoxantrone (Kaffaroni, et al. (2006) Neurol. Sci. 27 Suppl. 1:S13-7), which have been suggested to mediate the secondary inflammatory response, there has been no indication that these agents affect the primary etiological agent.

There is increasingly compelling evidence that MAP may be zoonotic (Greenstein & Collins (2004) Lancet 364(9432):396-7) and a human pathogen in gastrointestinal disease (Greenstein (2005) supra) and other diseases as well. There is an additional indication that in man, MAP is systemic and not confined to the gastrointestinal tract (Naser, et al. (2000) Am. J. Gastroenterol. 95(4):1094-5; Naser, et al. (2004) Lancet 364(9439):1039-1044). It is suggested that the reason MAP is zoonotic and has been missed as an etiological agent is that the medical profession has been unknowingly treating MAP with anti-inflammatory agents (e.g., 5-amino salicylic acid, methotrexate, and 6-mercaptopurine), which in fact have anti-MAP activity (Greenstein, et al. (2007) PLoS ONE 2:e161; Greenstein, et al. American Society of Microbiology 2007, Toronto, Canada). It is therefore of concern that viable MAP is found in the food chain (Eltholth, et al. (2009) J. Appl. Microbiol. 107:1061-1071), including pasteurized milk (Ellingson, et al. (2005) supra), and potable chlorinated municipal water (Mishina, et al. (1996) Proc. Natl. Acad. Sci. USA 93:9816-9820).

Accordingly, from the perspective of both animal and human health, control of Johne's disease is desirable. However, governmental agencies have been reluctant to initiate global Johne's disease vaccination programs over concern for the loss of ability to diagnose tuberculosis using skin testing.

SUMMARY OF THE INVENTION

The present invention is a method for producing a vaccine for immunizing a subject against mycobacterial infection by admixing (a) at least one Mycobacterium avium subspecies paratuberculosis (MAP) antigen, or attenuated or killed MAP; (b) at least one antigen isolated from a member of the M. tuberculosis complex (MTC), or an attenuated or killed mycobacterium from the MTC; and (c) a suitable carrier. In one embodiment, the attenuated or killed MAP is cell wall-competent or cell wall-deficient. In another embodiment, the MAP antigen is GroES, AhpD, 32 kDa antigen, kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, AhpC antigen or 65 kDa antigen. In a further embodiment, the member of the MTC is selected from the group of M. tuberculosis, M. bovis, M. bovis Calmette-Guérin, M. africanum, M. canetti, M. caprae, M. pinnipedii and M. microti.

Vaccines and methods for immunizing a subject against mycobacterial infection, preventing or treating mycobacterial infection, and preventing a disease associated with a mycobacterial infection in human and non-human subjects are also provided.

DETAILED DESCRIPTION OF THE INVENTION

Epidemiological analysis identifies a parallelism in the increasing incidence of Crohn's disease, ulcerative colitis and Multiple Sclerosis (Green, et al. (2006) supra). In Alzheimer's disease the use of “anti-inflammatories” shows therapeutic benefit (Rogers, et al. (1993) Neurology 43(8):1609-11). Additionally, there is the suggestion that rheumatoid arthritis is protective against Alzheimer's disease (McGeer, et al. (1990) Lancet 335(8696):1037). Analogous to lepromatous leprosy (Hansen (1874) Norsk Magazin for Laegevidenskaben 4:1-88) and tuberculoid leprosy, it is now posited that Multiple Sclerosis and perforating Crohn's disease (Gilberts, et al. (1994) Proc. Natl. Acad. Sci. USA 91(126):12721-12724) are the “acute” forms of a Mycobacterium avium subspecies paratuberculosis (MAP; basonym M. paratuberculosis) infection, whereas Alzheimer's Disease and obstructive Crohn's or ulcerative colitis are the chronic forms of a MAP infection. It is further posited that a causative relationship between MAP and diseases such as IBD and Multiple Sclerosis have been missed because it has not been appreciated that standard “immunomodulatory” treatment regimes, whose mechanisms of actions are unknown or speculated upon, are in fact effective because they are treating a MAP infection. It is posited that MAP is also responsible for a variety of diseases where an infectious etiology has been suggested, e.g., sarcoidosis, ankylosing spondylitis, psoriasis, and psoriatic arthritis and rheumatoid arthritis. Coincidentally, these diseases are often treated with “immunomodulatory” and “anti-inflammatory” agents that have now been shown to interfere with the growth kinetics of MAP.

While some reports have indicated that high-temperature short-time pasteurization does not effectively kill MAP in milk (Grant, et al. (1998) Lett. Appl. Microbiol. 26:166-170; Grant, et al. (1999) Lett. Appl. Microbiol. 28:461-465), killing by turbulent-flow conditions has been demonstrated (Stabel, et al. (1997) Appl. Environ. Microbiol. 63:4975-4977). Given the identification of potential sources of infection and that MAP is widespread over the industrialized as well as non-industrialized world and, a multipronged approach including vaccines, antibiotics, and public health measures are needed to control and prevent MAP infections as well as infections by one or more members of the M. tuberculosis complex (MTC). Accordingly, the present invention provides vaccines and methods for immunizing human and non-human subjects against mycobacterial infection.

As is known in the art, mycobacteria that cause human and/or animal tuberculosis (TB) are grouped together within the Mycobacterium tuberculosis complex. Members of the M. tuberculosis complex include M. tuberculosis, M. bovis, M. bovis Calmette-Guérin (BCG), M. africanum, M. canetti, M. caprae, M. pinnipedii and M. microti (Huard, et al. (2006) J. Bacteriol. 188:4271-4287). In one embodiment of the present invention, the instant vaccine and methods are used in the prevention and/or treatment of MAP and M. tuberculosis infection. In another embodiment, the instant vaccine and methods are used in the prevention and/or treatment of MAP and M. bovis infection. In yet a further embodiment, the instant vaccine and methods are used in the prevention and/or treatment of MAP, M. tuberculosis and M. bovis infection.

For the purposes of the present invention, a vaccine is intended to include whole cells, which in the case of MAP can be either cell wall-competent or cell wall-deficient; cell extracts; isolated protein (i.e., a subunit vaccine); or combinations thereof. Whole cell vaccines can be produced from mycobacteria that have been attenuated or have been killed. Attenuated means that the microorganisms are treated to reduce virulence, but maintain viability. Mycobacteria can be attenuated using any conventional strategy. For example, serial passage or long-term maintenance of the organism in culture media can be employed to attenuate mycobacteria. Live attenuated vaccines have the advantage of mimicking the natural infection enough to trigger an immune response similar to the response to the wild-type organism. Such vaccines generally provide a high level of protection, especially if administered by a natural route, and some may only require one dose to confer immunity. In the case of MAP, which exists in humans in the cell wall-deficient state, a vaccine that targets this obligate intracellular form is desirable. By way of illustration, cell wall-competent and cell wall-deficient (i.e., spheroplasts) vaccine preparations have been shown to reduce lesion scores associated with Johne's Disease in baby goats (Hines, et al. (2005) 8^(th) International Colloquium on Paratuberculosis, Copenhagen, Denmark). Attenuated M. tuberculosis strains are described, for example, in U.S. Pat. No. 7,722,861, wherein stains are genetically engineered to be auxotrophic for a vitamin.

In contrast to an attenuated vaccine, a vaccine containing killed mycobacteria means that the microorganisms are no longer viable, but are still capable of eliciting an immune response in the target animal. Mycobacteria can be killed using a number of different agents including, but not limited to, formalin, azide, freeze-thaw, sonication, heat treatment, sudden pressure drop, detergent (especially non-ionic detergents), lysozyme, phenol, proteolytic enzymes, propiolactone, Thimerosal (see, U.S. Pat. No. 5,338,543), and binary ethyleneimine (see, U.S. Pat. No. 5,565,205). By way of illustration, vaccination of calves with a heat-killed field strain of MAP results in high concentrations of IFN-γ and better protection against a MAP challenge exposure than does a commercially available vaccine (Uzonna, et al. (2002) Proc. 7^(th) Intl. Coll. Paratuberculosis; Juste (ed)).

In addition, or as an alternative to a vaccine containing attenuated or killed mycobacteria, a subunit vaccine can be employed. Any known mycobacterial antigen, or antigen fragment thereof, commonly employed in veterinary medicine can be used in the vaccine and methods of the present invention.

Examples of suitable MAP antigens include, but are not limited to, the antigens listed in Table 1.

TABLE 1 SEQ Size ID MAP protein Characteristic (kDa) NO: GroES Heat shock protein 10 1 AhpD Alkyl hydroperoxide reductase D 19 2   32-kDa antigen Fibronectin binding properties, secreted 32   34-kDa antigen Cell wall antigen, B-cell epitope 34 3   34-kDa antigen Serine protease 34 4 34.5-kDa antigen Cytoplasmic protein 34.5   35-kDa antigen Immunodominant protein 35   36-kDa antigen p36 antigen 36 5   42-kDa antigen Cytoplasmic protein 42 44.3-kDa antigen Soluble protein 44.3 AhpC Alkyl hydroperoxide reductase C 45 6   65-kDa antigen GroEL heat shock protein 65 7

The 32-kDa secreted protein with fibronectin binding properties has been implicated in protective immunity (Andersen, et al. (1991) Infect. Immun. 59:1905-1910; El-Zaatari, et al. (1994) Curr. Microbiol. 29:177-184) and the 34-kDa cell wall antigenic protein is homologous to a similar immunogenic protein in M. leprae (De Kesel, et al. (1992) Scand. J. Immunol. 36:201-212; De Kesel, et al. (1993) J. Clin. Microbiol. 31:947-954; Gilot, et al. (1993) J. Bacteriol. 175:4930-4935; Silbaq, et al. (1998) Infect. Immun. 66:5576-5579). The seroreactive 34-kDa serine protease expressed in vivo by MAP has also been described (Cameron, et al. (1994) Microbiology 140:1977-1982; however, this antigen is different from the 34-kDa antigen described above. Another strongly immunoreactive protein of kDa has also been identified in M. avium complex isolates, including MAP (El-Zaatari, et al. (1997) J. Clin. Microbiol. 35:1794-1799). A more thoroughly characterized protein of 65 kDa from MAP is a member of the GroEL family of heat shock proteins (El-Zaatari, et al. (1994) Curr. Microbiol. 29:177-184; El-Zaatari, et al. (1995) Clin. Diagn. Lab. Immunol. 2:657-664). Like the GroES proteins, the GroEL antigens from other mycobacteria are highly immunogenic (Shinnick (1987) J. Bacteriol. 169:1080-1088; Thole, et al. (1987) Infect. Immun. 55:1466-1475; Thole, et al. (1988) Infect. Immun. 56:1633-1640).

The alkyl hydroperoxide reductases C and D (AhpC and AhpD) have also been characterized as immunogenic proteins of MAP (Olsen, et al. (2000) Infect. Immun. 68:801-808). Unlike other mycobacteria, large amounts of these antigens are produced by MAP when the bacilli are grown without exposure to oxidative stress. AhpC is the larger of the two proteins and appears to exist as a homodimer in its native form since it migrates at both 45 and 24 kDa under denaturing conditions. In contrast, AhpD is a smaller monomer, with a molecular mass of about 19 kDa. Antiserum from rabbits immunized against AhpC and AhpD reacted only with MAP proteins and not with proteins from other mycobacterial species, indicating that antibodies against these proteins are not cross-reactive. Furthermore, peripheral blood monocytes from goats experimentally infected with MAP were capable of inducing gamma interferon (IFN-γ) responses after stimulation with AhpC and AhpD, confirming their immunogenicity (Olsen, et al. (2000) Infect. Immun. 68:801-808).

Antigenic proteins of M. tuberculosis are known in the art and include but are not limited to, PirG protein encoded by the Mtb gene Rv3810; PE-PGRS protein encoded by the Mtb gene Rv3367; PTRP protein encoded by the Mtb gene Rv0538; MtrA protein encoded by the Mtb gene Rv3246c; MTb81, Mo2, FL TbH4, HTCC#1 (Mtb40), TbH9, MTCC#2 (Mtb41), DPEP, DPPD, TbRa35, TbRa12, MTb59, MTb82, Erd14 (Mtb16), DPV (Mtb8.4), MSL (Mtb9.8), MTI (Mtb9.9A, also known as MTI-A), Ag85B, ESAT-6, and α-crystalline antigens of M. tuberculosis. In some embodiments, the antigenic protein provides cross-protection against M. tuberculosis and M. bovis, i.e., antibodies to said protein recognize the protein from both M. tuberculosis and M. bovis. In other embodiments, the antigenic protein is specific for M. tuberculosis and absent from the genome of BCG. Examples of such antigens include M. tuberculosis BCG Negative polypeptides, MTBN1-MTBN8. These and other antigens are described, for example, in U.S. Pat. Nos. 7,745,141; 7,579,141; and 7,311,922, incorporated herein by reference.

Antigenic proteins of M. bovis are also known in the art. For example, U.S. Pat. No. 7,670,609 describes a recombinant Bacille Calmette-Guerin (BCG) subunit-based vaccine.

Antigenic proteins disclosed herein, can be prepared and isolated by any conventional method including recombinant production. The term isolated does not require absolute purity; rather, it is intended as a relative definition, and can include preparations that are highly purified or preparations that are only partially purified. When recombinantly produced, antigenic proteins of the invention can also be produced as fusion proteins containing more than one antigen (e.g., fusion of antigen 85B (Ag85B) and ESAT-6) or fusion proteins containing an antigen in combination with an adjuvant or carrier protein.

It is contemplated that various combinations of antigen proteins, and/or attenuated and/or killed mycobacteria can be employed. By way of illustration, a vaccine of the invention can be composed of heat-killed MAP in combination with attenuated BCG. As another example, a vaccine of the invention can include an antigenic protein from MAP in combination with attenuated BCG and proteins Ag85B and ESAT-6 from M. tuberculosis.

Vaccines of the present invention are prepared using routine methods. Generally, vaccines are prepared as injectables, in the form of aqueous solutions or suspensions. Vaccines in an oil base are also well-known such as for inhalation. Solid forms which are dissolved or suspended prior to use can also be formulated. Suitable carriers, diluents and excipients are generally added that are compatible with the active ingredients and acceptable for use in humans and non-human animals. Examples of such carriers include, but are not limited to, water, saline solutions, dextrose, or glycerol. Carriers can also include liposomes or microspheres. Combinations of carriers can also be used. For example, prime immunization with BCG and a subunit vaccine (proteins Ag85B and ESAT-6) in liposomes followed by boosting with the subunit vaccine in conventional adjuvant has been shown to result in an increase in the protective efficacy of up to 7-fold compared with BCG alone and 3-fold compared with unaugmented BCG boosted by subunit vaccine (Dietrich, et al. (2007) J. Immunol. 178:7321-3730). A generally recognized compendium of methods and ingredients of vaccine compositions is Remington: The Science and Practice of Pharmacy, Alfonso R. Gennaro, editor, 20th ed. Lippincott Williams & Wilkins: Philadelphia, Pa., 2000.

Vaccine compositions can further incorporate additional substances to stabilize pH, or to function as adjuvants, wetting agents, or emulsifying agents, which can serve to improve the effectiveness of the vaccine. Examples of suitable adjuvants include, but are not limited to, aluminum salts; Incomplete Freund's adjuvant; threonyl and n-butyl derivatives of muramyl dipeptide; lipophilic derivatives of muramyl tripeptide; monophosphoryl lipid A; 3′-de-O-acetylated monophosphoryl lipid A; cholera toxin; QS21; phosphorothionated oligodeoxynucleotides with CpG motifs and adjuvants disclosed in U.S. Pat. No. 6,558,670.

Vaccines are generally formulated for parenteral administration and are injected either subcutaneously or intramuscularly. Vaccines can also be formulated as suppositories or for oral or nasal administration using methods known in the art. For example,

The amount of vaccine sufficient to confer immunity to pathogenic mycobacteria is determined by methods well-known to those skilled in the art. This quantity will be determined based upon the characteristics of the vaccine recipient and the level of immunity required. Typically, the amount of vaccine to be administered will be determined based upon the judgment of a skilled physician or veterinarian. Where vaccines are administered by subcutaneous or intramuscular injection, a range of 0.5 to 500 μg purified protein can be given.

The present invention is also directed to a vaccine in which an antigenic protein, or antigenic fragment thereof, is delivered or administered in the form of a polynucleotide encoding the protein or fragment (i.e., a DNA vaccine). In DNA vaccination, the subject is administered a polynucleotide encoding a antigenic protein that is then transcribed, translated and expressed in some form to produce strong, long-lived humoral and cell-mediated immune responses to the antigen. The polynucleotide can be administered using viral vectors or other vectors, such as liposomes, and can be combined with an acceptable carrier.

In addition, the proteins of the present invention can be used as antigens to stimulate the production of antibodies for use in passive immunotherapy, for use as diagnostic reagents, and for use as reagents in other processes such as affinity chromatography.

The present invention also embraces a method of using the instant vaccine as a means of immunizing animals, including humans and non-human animals such as sheep and cattle, against mycobacterial infection. In accordance with such a method, a vaccine containing mycobacterial antigens and/or attenuated and/or killed mycobacteria is administered to a subject in an amount effective to stimulate a measurable immune response. A measurable immune response can include a humoral response (e.g., production of antibodies to a particular antigen) or cell-mediate immune response (e.g., elicitation of a T cell response as determined by the production of cytokines such as IFN-gamma or IL-10).

In so far as the vaccine disclosed herein can be used to immunize a subject against mycobacterial infection, the present invention also provides for a method of preventing or treating mycobacterial infection, as well as a disease associated with mycobacterial infection. Such methods involve administering to a subject (humans and non-human animals) a vaccine containing at least one mycobacterial antigens and/or attenuated and/or killed mycobacteria, as disclosed herein, in an amount effective to prevent or attenuate said mycobacterial infection or symptoms of the mycobacterial-associated disease. In using the methods of the invention, the disease to be prevented or treated is desirably ulcerative colitis, irritable bowel syndrome, Crohn's Disease, Multiple Sclerosis, Alzheimer's Disease, sarcoidosis, ankylosing spondylitis, psoriasis, psoriatic arthritis rheumatoid arthritis, tuberculosis, and/or Johne's disease.

The invention is described in greater detail by the following non-limiting examples.

EXAMPLE 1 Prevalence of Johne's Disease in Vaccinated and Unvaccinated Ovine

Methods.

Data on the number of Ovine Johne's Disease (OJD) infected herds detected in New South Wales (NSW), Australia from 1980 to December 1998 were obtained. Positive herds were identified by both on-farm testing and confirmatory histopathology.

In 20 abattoirs in NSW, from November 1999 to December 2009, all consignments of sheep ≧2 years of age sent for slaughter were examined for the presence of OJD using methods known in the art (Bradley & Cannon (2005) Aust. Vet. J. 83:633-636). In brief, trained inspectors visually and by palpation examined the terminal ileum and adjacent lymph nodes of the animals. Positive tissues were then further examined histopathologically using Ziehl (Ziehl (1882) Dtsch. Med. Wschr. 8:451)-Neelsen (Neelsen (1883) Zbl. Med. Wiss. 21) staining. This method has a 74-87% individual animal sensitivity, and a 97-98% specificity (Bradley & Cannon (2005) supra). The higher values were found in areas designated as “High prevalence” (Bradley & Cannon (2005) supra).

Data collected by the inspectors included: the name and location of the Abattoir; date killed; consignment reference (Lot number); the total number of animals inspected; the number or estimated percentage of lesions grossly resembling OJD; the area of origin of the sheep and/or the property identification code (where available), which defines the Local Government Area and the property locality; the age (minimum 2 years or older); and sex of the animals.

OJD Prevalence Regions (“High”, “Medium” and “Low”) have been established by the NSW Department of Primary Industries. A maximum of three samples per consignment were submitted for histopathology. During the course of this study there was an evolution in the tissues examined. Initially multiple sites were examined and sampled (terminal ileum, ileo-caecal valve and associated lymph nodes.) Subsequently, only the terminal ileum was examined because of the large number of animals involved and minimal loss of sensitivity.

Consignments were initially classified on the basis of histopathology as positive (P), negative (N) or inconclusive (I). Samples were declared as Inconclusive when no Ziehl-Neelsen acid-fast organisms were detected despite the presence of granulomas typical of OJD. Consignments identified as “Inconclusive” were removed from the dataset with the following exception. When a consignment included inconclusive histopathology, these were attributed to OJD if other lesions from the same consignment were Ziehl-Neelsen positive or if OJD had been confirmed in the flock within the prior 2 years. Such flocks are designated as “Inconclusive Positive” (IP). P and IP are analyzed as Positive for the purpose of this report.

To account for other causes of intestinal abnormalities (e.g. coccidiosis, parasitism, salmonellosis, bacterial enteritis, etc.) the calculated number of lesions in positive lines were corrected pro-rata according to the number of lesions that were negative versus positive on histopathology.

Data for the units of GUDAIR® vaccine used were obtained from the Veterinary Authorities in NSW and sales data provided by the distributors CSL (Victoria, Australia) and Pfizer Australia.

Results.

There was a progressive increase in the incidence of OJD starting in 1980 in NSW with acceleration in the incidence over the next two decades. By 1998, 204 flocks were newly diagnosed with OJD, when the cumulative total of infected flocks was 441. Within Australia, the highest prevalence of OJD was in New South Wales and Victoria.

From 1999 to 2009, there were 33,735 total consignments of sheep sent to abattoirs, of which 40% (13,569) were from the High Prevalence Region (Table 2). A total of 7,807,937 carcasses were inspected, of which 39% (3,031,531) were from the High Prevalence region (Table 3). OJD was identified in 13% (4,454 (Table 4)/33,735 (Table 2)) of all consignments, of which 95% (4222/4454; Table 4) were from the High prevalence region. Within the High Prevalence region itself, 31% of consignments (4,222 (Table 4)/13,569 (Table 2)) were positive for OJD. A total of 1,212,859 carcasses were inspected in the positive consignments, of which 95% (1,150,196/1,212,859 (Table 5)) were from the High Prevalence region. Using established criteria, 46,259 animals had OJD, of which 96% (44,374/46,259 (Table 6)) were from the High Prevalence region. Within the High Prevalence region, an average of 3.8% (44,374 (Table 6)/1,150,196 (Table 5)) of carcasses had OJD lesions.

TABLE 2 Year High Medium Low Total/yr. 1999 150 12 68 231 2000 2171 294 2400 4991 2001 1656 208 1979 4043 2002 1879 163 1751 3917 2003 986 139 1084 2303 2004 1204 105 1340 2670 2005 747 89 1224 2065 2006 1640 132 2006 3785 2007 1276 235 2316 3829 2008 1025 167 2004 3196 2009 835 54 1816 2705 Total 1999-2009 13569 1598 17988 33735 The numbers of consignments from 1999-2009 stratified by region of OJD prevalence region and with the total of the three regions.

TABLE 3 Year High Medium Low Total/Yr 1999 33,102 3,224 20,163 56,489 2000 442,298 42,807 614,223 1,099,328 2001 350,731 28,443 511,640 890,814 2002 398,049 28,725 421,616 848,390 2003 191,606 25,097 220,764 437,467 2004 258,536 23,817 300,429 582,782 2005 164,839 20,677 300,093 485,609 2006 461,572 31,334 507,132 1,000,038 2007 292,935 57,749 576,465 927,149 2008 243,764 39,124 507,008 789,896 2009 194,099 11,536 484,340 689,975 Total 11 years 3,031,531 312,533 4,463,873 7,807,937 The numbers of carcasses inspected from 1999-2009 stratified by New South Wales Prevalence Region of OJD. Total per year (right hand column) and Cumulative Total per Prevalence Region from 1999-2009 (bottom row) are included.

TABLE 4 Year High Medium Low (+)/Year 1999 41 2 1 44 2000 421 6 10 438 2001 471 11 13 496 2002 667 11 8 689 2003 330 12 3 346 2004 395 17 6 418 2005 189 4 10 203 2006 634 8 14 656 2007 480 20 16 516 2008 346 20 16 382 2009 248 10 8 266 Total (+) 11 Years 4222 121 105 4454 The numbers of consignments where OJD was detected from 1999-2009 stratified by New South Wales Prevalence Region. Total per year (right hand column) and Cumulative Total per Prevalence Region from 1999-2009 (bottom row) are included.

TABLE 5 Year High Medium Low Total/Yr 1999 11,893 495 288 12,676 2000 104,047 902 4,618 109,567 2001 106,992 2,740 3,600 113,332 2002 153,454 1,997 2,491 157,942 2003 77,920 2,879 1,455 82,254 2004 100,276 4,285 1,896 106,457 2005 60,667 1,300 2,212 64,179 2006 221,343 1,728 4,315 227,386 2007 141,561 6,366 4,141 152,068 2008 98,344 4,634 5,965 108,943 2009 73,699 2,449 1,907 78,055 Grand Total 1,150,196 29,775 32,888 1,212,859 The numbers of sheep inspected in consignments where OJD was detected from 1999-2009 stratified by New South Wales Prevalence Region. Total per year (right hand column) and Cumulative Total per Prevalence Region from 1999-2009 (bottom row) are included.

TABLE 6 Year High Medium Low Total/yr 1999 1145 26 1 1,172 2000 9789 132 75 9,996 2001 5914 213 72 6,199 2002 8794 23 22 8,839 2003 3805 205 181 4,190 2004 4025 214 14 4,253 2005 1437 15 57 1,509 2006 3530 20 26 3,576 2007 2445 88 41 2,574 2008 2039 168 94 2,302 2009 1449 139 59 1,647 Total in 11 years 44374 1243 642 46,259 The numbers of sheep in positive consignments where OJD lesions were detected from 1999-2009 stratified by New South Wales Prevalence Region. Total per year (right hand column) and Cumulative Total per Prevalence Region from 1999-2009 (bottom row) are included.

Initially, vaccination in NSW began in late 1999 in a major trial (Reddacliff, et al. (2006) Vet. Microbiol. 115:77-90). From 2000-2002, by special permit limited to 50 flocks (total 155,523 sheep), vaccination was offered to owners of heavily infected flocks that had previously suffered a minimum of 5% annual mortality consequent to OJD. In April 2002, OJD vaccination was approved and registered for Australia. Administration began more widely on a voluntary basis. By 2009, a total of 10.7 million doses had been administered, of which 93% (9.8 million) were administered in the region of High Prevalence (Table 7). In the High Prevalence Region, the maximal number of vaccinations administered was in 2003, 1.7 million (Table 7). There has been a gradual, and erratic, decline in the number of yearly doses administered falling to 0.96 million doses in the High Prevalence region by 2009 (Table 7). In contrast, there has been a progressive increase, albeit at a far lower number, in the number of vaccinations administered in the region of Medium Prevalence rising 88% (from 50 to 94 thousand) from 2003 to 2009 (Table 7).

TABLE 7 Year High Medium Low All 1999 — — — — 2000 — — — — 2001 398,399 7,488 5,214 411,100 2002 943,057 17,443 609 961,109 2003 1,656,569 49,509 11,796 1,717,873 2004 1,553,554 69,891 45,916 1,669,360 2005 1,545,161 65,117 50,073 1,660,350 2006 1,191,433 67,198 44,818 1,303,449 2007 538,850 55,450 10,450 604,750 2008 1,002,650 94,100 35,150 1,131,900 2009 955,450 94,700 49,800 1,099,950 Total 2001/9 9,953,073 533,894 258,975 10,745,941 The numbers of vaccinations sold in New South Wales stratified by OJD Prevalence Region. Total per year (right hand column) and Cumulative Total per Prevalence Region from 1999-2009 (bottom row) are included. No Vaccinations were performed in 1999 or 2000.

During the course of the study the percentage of consignments that were positive remained erratically constant (High Prevalence Region: 27% in 1999 to 30% in 2009; Table 4) In noteworthy contrast, the % of animals that were positive for OJD in the High Prevalence Region fell progressively (High Prevalence Region 3.5% in 1999 to 0.75% 2009). In contrast, a countervailing trend was seen in the Medium Prevalence Region. Toward the end of the study, albeit with far fewer numbers, starting in 2005, there was an increase in the % positive consignments (Table 4). The number of animals positive as a % of the total number of animals inspected, increased from 0.06% in 2006 to 1.2% in 2009 (Table 6).

It was subsequently determined whether there was an association between the use of vaccination and trends in the incidence of OJD. From the time of institution of vaccination, there was a progressive decrease in the % lesions (+) per consignment (+). A more detailed analysis showed that fewer animals/consignment were infected as vaccination proceeded. The decrease was most pronounced when >10% of lesions were positive in a positive consignment (16% in 2001 falling to 4% by 2009. In contrast, there was a progressive increase in fewer animals per consignment being infected as vaccination proceeded (e.g. <1% of animals infected/infected consignment=24% in 2001 rising to 48% by 2009.

Conclusion:

Controlling Johne's Disease is important for the agricultural industry and veterinary community. Despite pilot studies showing Johne's Disease control with herd, animal and stool management (Collins, et al. (2010) J. Dairy Sci. 93:1638-1643), the increasing prevalence of Johne's Disease in cattle remains an obvious cause for concern.

The data herein show that prior to the initiation of vaccination, particularly in the High Prevalence areas, OJD in NSW was increasing. Following the institution of OJD vaccination program, a region-wide decrease in the prevalence and incidence of OJD is observed. It should however be noted that there are no similar encouraging results of a decrease in bovine Johne's Disease in the same geographical region during the same period.

The decrease in Johne's Disease in the High Prevalence Region was not replicated in the Medium Prevalence Region. These data may indicate that the Medium region may transitioning to a High Prevalence status.

Governmental agencies have been reluctant to initiate global Johne's Disease vaccination programs. The most compelling concern is the loss of ability to diagnose tuberculosis using skin testing. However, standard pasteurization of animal products satisfactorily kills M. bovis and M. tuberculosis. In contrast, MAP is not reproducibly killed by standard pasteurization. Therefore, a combination vaccine would be of use in addressing these problems.

EXAMPLE 2 Anti-Mycobacterial Vaccine

Mice (10 per group), e.g., wild-type and/or IL-18 deficient mice (Momotani, et al. (2002) Proc. 7^(th) Intl. Coll. Paratuberculosis, Juste (ed)) are immunized intraperitoneally (i.p.) with either AhpC or AhpD protein (15 μg in 50 μl PBS (phosphate-buffered saline) in combination with an Ag85B-ESAT-6 fusion protein (15 μg in 50 μl PBS) emulsified in 50 μl complete Freund's adjuvant (CFA)). A group of 10 mice are sham-immunized with PBS and CFA only.

A second immunization of 15 μg of each antigen with incomplete Freund's adjuvant (IFA) is administered 3 weeks later (with the sham-immunized group receiving PBS and IFA).

Blood is drawn at weeks 5 and 7. Sera from each group are pooled for analysis of antigen-specific antibody production by ELISA. Mice are challenged at week 8 by intraperitoneal injection of MAP and M. tuberculosis. Mice are monitored for signs and symptoms of disease.

Data will indicate that immunization of mice with either recombinant AhpC or AhpD proteins in combination with the Ag85B-ESAT-6 fusion protein elicits a response capable of protecting against MAP and M. tuberculosis infection.

EXAMPLE 3 Immunogenicity of Anti-Mycobacterial Vaccine in Humans

Sera from patients with culture-proven MAP infection are used in western blot analysis containing recombinant AhpC or AhpD protein.

The results of this analysis will demonstrate that sera from patients with MAP infections exhibit reactivity with either AhpC or AhpD, thereby indicating that AhpC and AhpD are recognized by the human immune system and suggest that antibodies able to bind the AhpC or AhpD protein can be produced during natural MAP infection in humans. Further, this data provides evidence that AhpC and AhpD are expressed in vivo by MAP during infection, and thus can be available as targets for immunoprophylaxis, immunotherapy, or to provide immune responses in subjects vaccinated with these proteins. 

What is claimed is:
 1. A method for producing a vaccine for immunizing a subject against Mycobacterium avium subspecies paratuberculosis (MAP) and M. tuberculosis (MTB) infection comprising admixing (a) at least one isolated and purified MAP antigen, or attenuated or killed MAP, wherein the MAP antigen is GroES, AhpD, 32 kDa antigen, 34 kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, 65 kDa antigen or AhpC antigen and the attenuated or killed MAP is cell wall-competent or cell wall-deficient; (b) at least one MTB antigen, or an attenuated or killed MTB; and (c) a suitable carrier thereby producing a vaccine for the immunization against MAP and MTB infection.
 2. A method for immunizing a subject against Mycobacterium avium subspecies paratuberculosis (MAP) and M. tuberculosis (MTB) infection comprising administering to a subject a vaccine containing (a) at least one isolated and purified MAP antigen, or attenuated or killed MAP, wherein the MAP antigen is GroES, AhpD, 32 kDa antigen, 34 kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, 65 kDa antigen or AhpC antigen and the attenuated or killed MAP is cell wall-competent or cell wall-deficient; and (b) at least one MTB antigen, or an attenuated or killed MTB, thereby immunizing the subject against MAP and MTB infection.
 3. A method for treating Mycobacterium avium subspecies paratuberculosis (MAP) and M. tuberculosis (MTB) infection comprising administering to a subject a vaccine containing (a) at least one isolated and purified MAP antigen, or attenuated or killed MAP; and (b) at least one MTB antigen, or an attenuated or killed MTB, thereby treating MAP and MTB infection.
 4. The method of claim 3, wherein the attenuated or killed MAP is cell wall-competent or cell wall-deficient.
 5. The method of claim 3, wherein the MAP antigen is GroES, AhpD, 32 kDa antigen, kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, 65 kDa antigen or AhpC antigen.
 6. The method of claim 3, wherein the subject is a non-human animal.
 7. A method for preventing a disease associated with Mycobacterium avium subspecies paratuberculosis (MAP) and M. tuberculosis (MTB) infection comprising administering to a subject a vaccine containing (a) at least one attenuated or killed MAP, wherein the attenuated or killed MAP is cell wall-competent or cell wall-deficient; (b) at least one MTB antigen, or an attenuated or killed MTB, thereby preventing a disease associated with MAP and MTB infection.
 8. A method for preventing a disease associated with Mycobacterium avium subspecies paratuberculosis (MAP) and M. tuberculosis (MTB) infection comprising administering to a subject a vaccine containing (a) at least one isolated and purified MAP antigen, wherein the MAP antigen is GroES, AhpD, 32 kDa antigen, 34 kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, 65 kDa antigen or AhpC antigen; (b) at least one MTB antigen, or an attenuated or killed MTB, thereby preventing a disease associated with MAP and MTB infection.
 9. A vaccine comprising (a) at least one isolated and purified Mycobacterium avium subspecies paratuberculosis (MAP) antigen, or attenuated or killed MAP, wherein the MAP antigen is GroES, AhpD, 32 kDa antigen, 34 kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, 65 kDa antigen or AhpC antigen and the attenuated or killed MAP is cell wall-competent or cell wall-deficient; (b) at least one isolated and purified antigen from a member of the M. tuberculosis complex (MTC), or an attenuated or killed mycobacterium from the MTC; and (c) a suitable carrier.
 10. A vaccine consisting of: (a) at least one attenuated or killed Mycobacterium avium subspecies paratuberculosis (MAP), wherein the attenuated or killed MAP is cell wall-competent or cell wall-deficient; (b) at least one isolated and purified antigen from a member of the M. tuberculosis complex (MTC), or an attenuated or killed mycobacterium from the MTC; and (c) a suitable carrier.
 11. A vaccine consisting of: (a) at least one Mycobacterium avium subspecies paratuberculosis (MAP) antigen, wherein the MAP antigen is GroES, AhpD, 32 kDa antigen, 34 kDa antigen, 34.5 kDa antigen, 35 kDa antigen, 36 kDa antigen, 42 kDa antigen, 44.3 kDa antigen, 65 kDa antigen or AhpC antigen; (b) at least one isolated and purified antigen from a member of the M. tuberculosis complex (MTC), or an attenuated or killed mycobacterium from the MTC; and (c) a suitable carrier. 